4HCR: Human MAdCAM-1 D1D2

Crystal structure of human MAdCAM-1 D1D2 complexed with Fab PF-547659. Determined by X-ray diffraction at 2.3 Å resolution. Released 23 Jan 2013.

Method: X-ray diffraction
Resolution: 2.3 Å
Organism: Homo sapiens
Chains: 6
Atoms: 10,592
Mol. weight: 142 kDa
Released: 23 Jan 2013

Explore 4HCR in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4HCR contains 38 α-helices and 137 β-strands across 6 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chains A and B: 3 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	13
β-strand	12-16	5	14
β-strand	21-27	7	13
β-strand	36-40	5	14
β-strand	47-49	3	13
β-strand	55-59	5	13
α-helix	64-66	3
β-strand	68-76	9	14
β-strand	79-90	12	14
β-strand	91	1	15
β-strand	96-99	4	16
β-strand	103	1	17
β-strand	109-117	9	16
β-strand	118	1	15
β-strand	125-131	7	18
β-strand	134-135	2	18
β-strand	140-141	2	16
β-strand	145-148	4	16
β-strand	161-168	8	16
α-helix	169-171	3
α-helix	176-177	2
β-strand	179-188	10	18
β-strand	191-200	10	18
β-strand	201	1	17

Chain H: 7 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	1
β-strand	10-12	3	2
β-strand	18-25	8	1
α-helix	29-31	3
β-strand	33-39	7	2
β-strand	46-51	6	2
β-strand	58-60	3	2
β-strand	68-73	6	1
β-strand	78-83	6	1
α-helix	88-90	3
β-strand	92-101	10	2
β-strand	108-114	7	2
β-strand	115	1	1
β-strand	118-122	5	2
β-strand	128	1	3
α-helix	129-130	2
β-strand	131-135	5	4
β-strand	147-156	10	4
β-strand	157	1	3
β-strand	162-165	4	5
α-helix	166-168	3
β-strand	170	1	5
β-strand	174-176	3	4
α-helix	177-179	3
β-strand	180-181	2	4
β-strand	187-195	9	4
α-helix	199-202	4
β-strand	203	1	6
β-strand	206-211	6	5
α-helix	212-214	3
β-strand	216-221	6	5

Chain L: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	7
β-strand	10-13	4	8
β-strand	19-25	7	7
β-strand	30	1	9
β-strand	36	1	9
β-strand	38-43	6	8
β-strand	50-54	5	8
β-strand	58-59	2	8
α-helix	60	1
β-strand	67-72	6	7
β-strand	75-80	6	7
α-helix	85-87	3
β-strand	89-95	7	8
α-helix	101	1
β-strand	102-103	2	8
β-strand	107-111	5	8
β-strand	116	1	10
α-helix	117-118	2
β-strand	119-123	5	11
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	11
β-strand	145	1	10
β-strand	149-155	7	12
β-strand	158-159	2	12
α-helix	160	1
β-strand	164-168	5	11
α-helix	169-172	4
β-strand	178-187	10	11
α-helix	188-191	4
β-strand	196-203	8	12
β-strand	210-215	6	12

Chain M: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	19
β-strand	10-12	3	20
β-strand	18-25	8	19
α-helix	29-31	3
β-strand	33-39	7	20
β-strand	46-51	6	20
β-strand	58-60	3	20
β-strand	68-73	6	19
β-strand	78-83	6	19
α-helix	88-90	3
β-strand	92-99	8	20
β-strand	100-101	2	21
β-strand	108-110	3	21
β-strand	114	1	20
β-strand	118-122	5	20
β-strand	128	1	22
α-helix	129-130	2
β-strand	131-135	5	23
β-strand	146-156	11	23
β-strand	157	1	22
β-strand	162-165	4	24
α-helix	166-168	3
β-strand	174-176	3	23
α-helix	177-179	3
β-strand	180-181	2	23
β-strand	187-196	10	23
α-helix	197-199	3
β-strand	200	1	25
β-strand	203	1	25
β-strand	205-211	7	24
α-helix	212-214	3
β-strand	216-222	7	24

Chain N: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	26
β-strand	10-13	4	27
β-strand	19-25	7	26
β-strand	30	1	28
β-strand	36	1	28
β-strand	38-43	6	27
β-strand	50-54	5	27
β-strand	58-59	2	27
α-helix	60	1
β-strand	67-72	6	26
β-strand	75-80	6	26
α-helix	85-87	3
β-strand	89-95	7	27
α-helix	101	1
β-strand	102-103	2	27
β-strand	107-111	5	27
β-strand	116	1	29
α-helix	117-118	2
β-strand	119-123	5	30
α-helix	124-126	3
α-helix	127-131	5
β-strand	134-144	11	30
β-strand	145	1	29
β-strand	150-155	6	31
β-strand	158-159	2	31
α-helix	160	1
β-strand	164-168	5	30
α-helix	169-172	4
β-strand	178-187	10	30
α-helix	188-191	4
β-strand	196-202	7	31
β-strand	210-215	6	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
PF-547659 heavy chain	H, M	protein	229	Homo sapiens
PF-547659 light chain	L, N	protein	219	Homo sapiens
Mucosal addressin cell adhesion molecule 1	A, B	protein	209	Homo sapiens	Q13477 (AlphaFold model)

Sequence of entity 1 (H, M), FASTA

>4HCR_1 PF-547659 heavy chain (chains H, M)
QVQLVQSGAEVKKPGASVKVSCKASGYTFTSYGINWVRQAPGQGLEWMGWISVYSGNTNY
AQKVQGRVTMTADTSTSTAYMDLRSLRSDDTAVYYCAREGSSSSGDYYYGMDVWGQGTTV
TVSSASTKGPSVFPLAPCSRSTSESTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAV
LQSSGLYSLSSVVTVPSSNFGTQTYTCNVDHKPSNTKVDKTVERKCCVE

Sequence of entity 2 (L, N), FASTA

>4HCR_2 PF-547659 light chain (chains L, N)
DIVMTQTPLSLSVTPGQPASISCKSSQSLLHTDGTTYLYWYLQKPGQPPQLLIYEVSNRF
SGVPDRFSGSGSGTDFTLKISRVEAEDVGIYYCMQNIQLPWTFGQGTKVEIKRTVAAPSV
FIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSL
SSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC

Sequence of entity 3 (A, B), FASTA

>4HCR_3 Mucosal addressin cell adhesion molecule 1 (chains A, B)
VKPLQVEPPEPVVAVALGASRQLTCRLACADRGASVQWRGLDTSLGAVQSDTGRSVLTVR
NASLSAAGTRVCVGSCGGRTFQHTVQLLVYAFPNQLTVSPAALVPGDPEVACTAHKVTPV
DPNALSFSLLVGGQELEGAQALGPEVQEEEEEPQGDEDVLFRVTERWRLPPLGTPVPPAL
YCQATMRLPGLELSHRQAIPVLHHHHHHH

Primary citation

A Different Fold with an Integrin-Binding Loop Specialized for Flexibility in Mucosal Addressin Cell Adhesion Molecule-1. Springer, T., Yu, Y., Zhu, J. et al. To be published.

Other PDB entries of the same protein (UniProt Q13477 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4HBQ 1.4 Å, Crystal structure of a loop deleted mutant of Human MAdCAM-1 D1D2
4HD9 1.7 Å, Crystal structure of native human MAdCAM-1 D1D2 domain
1GSM 1.9 Å, A reassessment of the MAdCAM-1 structure and its role in integrin recognition.
1BQS 2.2 Å, The crystal structure of mucosal addressin cell adhesion molecule-1 (madcam-1)
4HC1 2.87 Å, Crystal structure of a loop deleted mutant of human MAdCAM-1 D1D2 complexed with Fab 10G3
9P95 3.05 Å, CryoEM structure of integrin alpha4beta7 bound to MAdCAM-1

Browse structure collections

About this viewer

MolViewer shows 4HCR directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.