1DX5

Crystal structure of the thrombin-thrombomodulin complex

Entity

Entity ID	Chain ID	Description	Type	Chain length	Formula weight	Number of molecules	DB Name (Accession)	Biological source	Descriptive keywords
1	A, B, C, D (A, B, C, D)	Thrombin light chain	polymer	36	4096.5	4	UniProt (P00734) Pfam (PF09396)	Homo sapiens (Human)	Coagulation factor II
2	E, F, G, H (I, J, K, L)	Thrombomodulin	polymer	118	12691.1	4	UniProt (P07204) Pfam (PF12662)	Homo sapiens (Human)	TM,Fetomodulin
3	I, J, K, L (M, N, O, P)	Thrombin heavy chain	polymer	259	29792.3	4	UniProt (P00734) Pfam (PF00089)	Homo sapiens (Human)	Coagulation factor II
4	M, P, S, SA, V (I, J, K, P, L)	FORMIC ACID	non-polymer		46.0	5	Chemie (FMT)
5	N, Q, T, W (I, J, K, L)	CALCIUM ION	non-polymer		40.1	4	Chemie (CA)
6	FA, LA, O, R, RA... (N, O, I, J, P...)	SODIUM ION	non-polymer		23.0	8	Chemie (NA)
7	EA, KA, QA, Y (N, O, P, M)	2-acetamido-2-deoxy-beta-D-glucopyranose	non-polymer		221.2	4	Chemie (NAG)
8	AA, BA, CA, DA, GA... (M, N, O, P)	L-alpha-glutamyl-N-{(1S)-4-{[amino(iminio)methyl]amino}-1-[(1S)-2-chloro-1-hydroxyethyl]butyl}glycinamide	non-polymer		395.9	16	BIRD (PRD_000288) Chemie (0GJ)
9	AB, BB, CB, DB, EB... (D, I, J, K, L...)	water	water		18.0	815	Chemie (HOH)

Sequence modifications

I, J, K, L: 345 - 462 (UniProt: P07204)

PDB	External Database	Details
Asp 364	Asn 382	conflict
Gly 456	Arg 474	conflict
Gln 457	His 475	conflict

M, N, O, P: 16 - 247 (UniProt: P00734)

PDB	External Database	Details
Ile 60	Thr 418	conflict

Contents of the asymmetric unit

Polymers	Number of chains	12
	Total formula weight	186319.6
Non-Polymers*	Number of molecules	37
	Total formula weight	7793.0
All*	Total formula weight	194112.6

*Water molecules are not included.